Re: [galaxy-dev] Error download composite dataset from history

Hi Ross Thanks a million, I hg-pull'ed it solved the problem!! Please push it to galaxy-dist? ;) I ran in another little bug though, but nothing serious, you might even have already spotted it by now: In lib/galaxy/web/framework/__init__.py the line 873 made the whole thing crash due to a

Re: [galaxy-dev] problems with location of filter bar in trackster

Hi Jeremy Thank you very much for your help. I will look into your suggestions. Regards, Hans On 01/18/2012 10:08 PM, Jeremy Goecks wrote: it works fine on the public server Good, this narrows down the problem to installing the -central script on your instance b/c main's copy of the

Re: [galaxy-dev] Error download composite dataset from history

Hi, L-A, 2012/1/19 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hi Ross Thanks a million, I hg-pull'ed it solved the problem!! Please push it to galaxy-dist? ;) Glad to hear it works - thanks for reporting back. I ran in another little bug though, but nothing serious, you might

[galaxy-dev] LDAP authentification

Hello, I'm trying to install galaxy on a apache server,and i have the same error message than David HOOVER when i tried to generate the authentification files. Thanks to David Hoover who gives me some helpful explanation. When i read the thread on gmod, it seems,that the problem is solved

Re: [galaxy-dev] LDAP authentification

Hi Sarah: I don't know what kind of LDAP you're talking to... I'm talking to Active Directory and this configuration works in that situation. Order allow,deny allow from all AuthType Basic AuthName NEB Credentials AuthBasicProvider

Re: [galaxy-dev] LDAP authentification

We also ran into this. Our local server configuration was case-sensitive and the LDAP uid key was converted to upper-case, so we used: RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e which fixed the problem. We found the solution by searching for 'AUTHENTICATE_uid', it appears to be a

Re: [galaxy-dev] LDAP authentification

Hi Brad, Hi Christopher, Thanks a lot. I'm talking to Open LDAP. I have changed RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e to RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e But I always have the same message /(Access to Galaxy is denied Galaxy is configured to authenticate users

Re: [galaxy-dev] LDAP authentification

Why do you need to create a proxy? The way I have ours set up is within a virtual host: VirtualHost Location / AuthName Helix Systems AuthType Basic AuthBasicProvider ldap AuthzLDAPAuthoritative off AuthLDAPUrl

Re: [galaxy-dev] LDAP authentification

Hello Sarah, Sarah Maman wrote, On 01/19/2012 10:49 AM: I'm talking to Open LDAP. I have changed RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e to RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e But I always have the same message /(Access to Galaxy is denied Galaxy is configured

Re: [galaxy-dev] LDAP authentification

David, This is the approach recommended on the wiki for performance: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy Would be nice if your alternative approach using virtual hosts were similarly documented. chris On Jan 19, 2012, at 10:01 AM, David Hoover wrote: Why do you need to

[galaxy-dev] job quotas

Hi, is it possible to restrict the number of concurrent jobs for a single user in a local instance of galaxy? I see that in the public site this feature is implemented, but I don't find documentation about how to implement this locally. I think it's not possible through pbs because all users

Re: [galaxy-dev] changeset inconsistency

Hi Hans, We're releasing a distribution today. If this is still the case with that distribution, let me know. There were branches that weren't showing up under newer versions of Mercurial. Hopefully this is all resolved in the latest. --nate On Jan 17, 2012, at 4:11 AM, Hans-Rudolf Hotz

Re: [galaxy-dev] Switching TorquePBSpro: qsub error 111 (cannot connect to server)

On Jan 16, 2012, at 5:22 AM, Louise-Amélie Schmitt wrote: Hello, We want to move Galaxy's jobs from our small TORQUE local install to a big cluster running PBS Pro. In the universe_wsgi.ini, I changed the cluster address as follows: default_cluster_job_runner = pbs:/// to:

Re: [galaxy-dev] how to set FTP quota?

Hi Leon, Jen is correct. As far as the FTP directory, we use the MaxStoreFileSize directive in ProFTPd to limit the size of any single file uploaded. --nate On Jan 17, 2012, at 10:22 PM, Jennifer Jackson wrote: Hi Leon, I can let you know that there is a hard limit of 50G per file

Re: [galaxy-dev] LDAP authentification

On Jan 19, 2012, at 10:49 AM, Sarah Maman wrote: Hi Brad, Hi Christopher, Thanks a lot. I'm talking to Open LDAP. I have changed RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e to RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e But I always have the same message /(Access to

Re: [galaxy-dev] Quota will not decrease with permanent delete

On Jan 16, 2012, at 8:31 AM, Peter Cock wrote: On Mon, Jan 16, 2012 at 1:20 PM, graham etherington (TSL) graham.ethering...@sainsbury-laboratory.ac.uk wrote: Hi Nate, We are getting quite large discrepancies between 'Size on disk' and 'Usage' numbers, so I've run the

Re: [galaxy-dev] samtools version detection issue

On Jan 18, 2012, at 5:28 PM, Matt Shirley wrote: Hi all. I'm sorry if this has been answered before, but I've searched and cannot find a solution other than add SAMtools to your PATH, which I already have done. I can invoke samtools from BASH while logged in as the galaxy user I set up

Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException

I haven't added any such delay after DrmCommunicationException however I have thought about increasing it in the job monitor function itself (site specific change, not suggesting it in the blessed galaxy repo).